The Virtual Brain Project

Source code for tvb.core.entities.transient.structure_entities

# -*- coding: utf-8 -*-
# TheVirtualBrain-Framework Package. This package holds all Data Management, and 
# Web-UI helpful to run brain-simulations. To use it, you also need do download
# TheVirtualBrain-Scientific Package (for simulators). See content of the
# documentation-folder for more details. See also
# (c) 2012-2017, Baycrest Centre for Geriatric Care ("Baycrest") and others
# This program is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software Foundation,
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# PARTICULAR PURPOSE.  See the GNU General Public License for more details.
# You should have received a copy of the GNU General Public License along with this
# program.  If not, see <>.
# When using The Virtual Brain for scientific publications, please cite it as follows:
#   Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide,
#   Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
#       The Virtual Brain: a simulator of primate brain network dynamics.
#   Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)

.. moduleauthor:: Ionel Ortelecan <>
.. moduleauthor:: Lia Domide <>

import json
from tvb.basic.config.utils import EnhancedDictionary

[docs]class StructureNode: """ This entity represents a node in the Tree of a Project related Structure. """ TYPE_FOLDER = "Folder" TYPE_FILE = "File" TYPE_INVALID = "Invalid" PREFIX_ID_NODE = "node_" PREFIX_ID_LEAF = "leaf_" PREFIX_ID_PROJECT = "projectID" SEP = "__" def __init__(self, nid, node_name, ntype=TYPE_FOLDER, meta=None, children=None): """ Constructor :param nid: Node Identifier (needs to be UQ) :param node_name: Node Display Name :param ntype: Node Type (influences the display mode in UI). :param meta: DataTypeMetaData instance. :param children: List of StructureNode entities or None. """ = nid = node_name self._type = ntype self.metadata = meta self.children = children @property
[docs] def has_children(self): """ Return TRUE when current node is with Child nodes. Return FALSE when current node is a leaf in Tree. """ return self.children and len(self.children) > 0
@property @property
[docs] def is_irelevant(self): """Check that current node is marked as not-relevant.""" if (self.metadata is not None and DataTypeMetaData.KEY_RELEVANCY in self.metadata and not self.metadata[DataTypeMetaData.KEY_RELEVANCY]): return True return False
[docs] def is_group(self): """ Check if meta_data has the transient is_link attribute set. """ return (self.metadata is not None and DataTypeMetaData.KEY_OP_GROUP_ID in self.metadata and self.metadata[DataTypeMetaData.KEY_OP_GROUP_ID] is not None)
[docs] def type(self): """ Type of a node it can be FOLDER, FILE or INVALID. """ return self._type
[docs] def metadata2tree(metadatas, first_level, second_level, project_id, project_name): """ Take a list of DataTypeMetaData entities as input. Create a tree of StructureNode entities, then convert it in JSON to display in UI. first_level and second_level represents the fields by which should be structured the tree. Those fields should exists into the data dict of each DataTypeMetaData object. """ levels = {} for meta in metadatas: level_one = str(meta[first_level]) level_two = str(meta[second_level]) if level_one not in levels: levels[level_one] = {level_two: [meta]} else: existent_sublevels = levels[level_one] if level_two not in existent_sublevels: levels[level_one][level_two] = [meta] else: levels[level_one][level_two].append(meta) forest = [] for level in sorted(levels.iterkeys()): sublevels = levels[level] level_children = [] for sublevel in sorted(sublevels.iterkeys()): metas = sublevels[sublevel] datas = [] for meta in metas: parent_name = meta[meta.KEY_NODE_TYPE] + " " if meta[meta.KEY_TAG_1]: parent_name = parent_name + " - " + meta[meta.KEY_TAG_1] if meta[meta.KEY_OPERATION_TAG]: parent_name = parent_name + " - " + meta[meta.KEY_OPERATION_TAG] parent = StructureNode(meta.gid, parent_name, meta=meta) if meta.invalid: parent._type = StructureNode.TYPE_INVALID else: parent._type = meta[meta.KEY_NODE_TYPE] datas.append(parent) sublevel_id = level.replace(" ", "") + StructureNode.SEP + sublevel.replace(" ", "") sublevel_name = StructureNode._prepare_node_name(sublevel, second_level) sublevel_node = StructureNode(sublevel_id, sublevel_name, children=datas) sublevel_node._type = StructureNode._capitalize_first_letter(second_level) level_children.append(sublevel_node) dir_name = StructureNode._prepare_node_name(level, first_level) level_node = StructureNode(level, dir_name, children=level_children) level_node._type = StructureNode._capitalize_first_letter(first_level) forest.append(level_node) json_children = StructureNode.__convert2json(forest, project_id) if len(json_children) > 0: result = '{data: [{ data: {title: "' + project_name + '"' result += ',icon: "/static/style/nodes/nodeRoot.png"},' result += 'state:"open", attr:{id:"' + StructureNode.PREFIX_ID_PROJECT result += '"}, children: [' + json_children + '] } ] }' else: result = '{data: [{ data: {title: "' + project_name + '"' result += ',icon: "/static/style/nodes/nodeRoot.png"}' result += ',attr:{id:"' + StructureNode.PREFIX_ID_PROJECT + '"}}]}' return result
@staticmethod def _prepare_node_name(name, level_filter): """ Process name. In case filter corresponds to STATE, then return display value for it. """ if level_filter == DataTypeMetaData.KEY_STATE: return DataTypeMetaData.STATES[name] return name @staticmethod def _capitalize_first_letter(word): """ :returns: same string, but with first letter capitalized. """ return word[0].upper() + word[1:] @staticmethod def __convert2json(nodes_list, project_id): """ Local method, for converting an internal Tree structure (of StructureNode entities) into a JSON object, ready for display into UI with JSTree. """ result = "" place_comma = False for node in nodes_list: json_node = '{data: {title:"' + ( if len( < 100 else[:95] + "...") json_node += '",icon: "/static/style/nodes/node' if node.is_group: json_node += 'Group.png"},' else: json_node += node.type + '.png"},' if node.metadata is None and node.has_children: json_node += ' state:"open", ' json_node += 'attr:{id:"' + StructureNode.PREFIX_ID_NODE + + '", separator: ">>", ' json_node += 'projectId:"' + str(project_id) + '"' if node.metadata is not None: meta_str = json.dumps(node.metadata) meta_str = meta_str.replace('{', '').replace('}', '') json_node += ',' + meta_str json_node += ', style: "' if node.is_irelevant: json_node += 'background-color: #666;' if node.is_link: json_node += 'font-style: italic;' json_node += '" }' if node.has_children: json_node += ', children:[' + StructureNode.__convert2json(node.children, project_id) + ']' json_node += '}' if place_comma: result += ',' place_comma = True result += json_node return result
[docs]class GenericMetaData(EnhancedDictionary): """ Wrap a dictionary of meta-data for generic entities - Operations, Project, or DataType. """ KEY_GID = "Gid" KEY_FILENAME = "file_name" def __init__(self, data=None): """ :param data: The actual dictionary to be wrapped by current entity. """ super(GenericMetaData, self).__init__() if data is not None: self.update(data) @property
[docs] def gid(self): """ :returns: current Global Identifier or None. """ if self.KEY_GID in self.keys(): return self[self.KEY_GID] return None
[docs] def file_name(self): """ :returns: name of the file where to store current data, or None. """ if self.KEY_FILENAME in self.keys(): return self[self.KEY_FILENAME] return None
[docs]class DataTypeMetaData(GenericMetaData): """ This object will be populated from meta-data stored on a particular DataType/Operation. It should contain enough information, to restore a DataType entity, without DB previous data required. """ KEY_STATE = "Data_State" STATES = {'RAW_DATA': 'Raw Data', 'INTERMEDIATE': 'Intermediate', 'FINAL': 'Final'} KEY_SUBJECT = "Data_Subject" DEFAULT_SUBJECT = "John Doe" KEY_BURST = "Burst_Reference" KEY_TAG_1 = "User_Tag_1_Perpetuated" KEY_TAG_2 = "User_Tag_2" KEY_TAG_3 = "User_Tag_3" KEY_TAG_4 = "User_Tag_4" KEY_TAG_5 = "User_Tag_5" KEY_MODULE = "Module" KEY_CLASS_NAME = "Type" KEY_AUTHOR = "Source_Author" KEY_OPERATION_TYPE = "Source_Operation_Category" KEY_DATE = "Creation_Date" KEY_OPERATION_TAG = "user_group" KEY_OP_GROUP_ID = "groupId" KEY_RELEVANCY = "Relevant" KEY_TITLE = "title" #Transient attributes KEY_NODE_TYPE = "DataType" KEY_DATATYPE_ID = "Datatypeid" KEY_INVALID = "datatype_invalid" KEY_COUNT = "count" KEY_LINK = "link" KEY_CREATE_DATA_MONTH = "createDataMonth" KEY_CREATE_DATA_DAY = "createDataDay" #operation details KEY_OPERATION_GROUP_NAME = "op_group_name" KEY_OPERATION_ALGORITHM = "Operation_Algorithm" KEY_FK_OPERATION_GROUP = 'fk_operation_group' def __init__(self, data=None, invalid=False): GenericMetaData.__init__(self, data) self.invalid = invalid @property
[docs] def subject(self): """ Return the name of the Subject if defined, or Default "John Doe". """ if self.KEY_SUBJECT not in self.keys(): return self.DEFAULT_SUBJECT return self[self.KEY_SUBJECT]
[docs] def create_date(self): """ Return the create date of this entity, if stored, or None otherwise. """ if self.KEY_DATE in self.keys(): return self[self.KEY_DATE] return None
[docs] def group(self): """ Return the group tag in which the operation was launched """ if self.KEY_OPERATION_TAG in self.keys(): return self[self.KEY_OPERATION_TAG] return None
[docs] def mark_invalid(self): """ Mark current meta-data as invalid. e.g. Because of a missing associated file. """ self.invalid = True
[docs] def merge_data(self, new_data): """ Update current state, from an external dictionary. """ if new_data is None: return for val in new_data: #Ignore transient entities if val != self.KEY_COUNT and val != self.KEY_OP_GROUP_ID: self[val] = new_data[val] ##### CLASS METHODS start Here ########################################
[docs] def get_filterable_meta(cls): """ Contains all the attributes by which the user can structure the tree of DataTypes. All the returned attributes should exists into the 'data' field of its corresponding DataTypeMetaData object. """ return [ {cls.KEY_NODE_TYPE: "Data Type"}, {cls.KEY_SUBJECT: "Subject"}, {cls.KEY_STATE: "State"}, {cls.KEY_OPERATION_TAG: "Operation group name"}, {cls.KEY_GID: "Unique Global Identifier"}, {cls.KEY_DATATYPE_ID: "Entity id"}, {cls.KEY_CREATE_DATA_DAY: "Create data day"}, {cls.KEY_CREATE_DATA_MONTH: "Create data month"}, {cls.KEY_OPERATION_ALGORITHM: "Operation algorithm"}, {cls.KEY_BURST: "Simulation name"}, {cls.KEY_TAG_1: "DataType Tag 1"}, {cls.KEY_TAG_2: "DataType Tag 2"}, {cls.KEY_TAG_3: "DataType Tag 3"}, {cls.KEY_TAG_4: "DataType Tag 4"}, {cls.KEY_TAG_5: "DataType Tag 5"} ]